The real advantage of PDF is that it is a final form document format. Truly WYSIWYG. Which is literally the anthesis of HTML which is completely separated (theoretically) from the display/formatting.
PDFs are treated that way, but it isn't really true. Due to the complexity of the format, there are many PDFs that will display differently in different viewers.
I don't see a problem with giving the document creator the option to go with a fluid or fixed layout and make the software default to fixed layout.
What are some good WYSIWYG vector standards, including the font department? It could be useful for a GUI markup standard also so that we can have platform-neutral GUI's and GUI's over HTTP.
The server side may still have a dynamic/flow layout engine, but calculated coordinates are sent to the client, keeping the client simpler and more predictable.
HTML and CSS theoretically have these properties, but if you asked someone in the publishing industry to layout a book with them they would either quit on the spot or hate you until their dying breath. That or they're a masochist and want to see if they could actually do it because it is theoretically possible.